Thousands of Londoners endured a gruelling commute on Tuesday as a result of an exercise to test the capital's Olympic rail capacity, which raised fresh fears about the transport network's ability to cope during the Games.

With the Olympics just over a fortnight away, Network Rail and Southeastern trains rehearsed their station management plans to see how five key stations – London Bridge, Cannon Street, Waterloo East, Charing Cross and Victoria – will cope with the increased passenger numbers.

London Bridge was most affected by the exercise, with a queuing system put in place and entry to the station confined to the forecourt on Railway Approach/London Bridge Street. Commuters complained of increased queues, missed connections due to longer walks between Underground and Network Rail services and of contractors guiding passengers sending them the wrong way. Many said they were also angry they had not been warned about the exercise– a claim denied by the rail operators.

Trevor Preston, 50, a civil engineer, said: "It's ridiculous. I've been sent back and forth. It's going to be chaos during the Olympics. There are so many people speaking on PA systems, it's complete confusion." Debbie Thraves, 50, travelling from Orpington to Waterloo East with her 72-year-old disabled mother, Maureen Harris, to visit a friend in hospital, said: "Nobody seems to know what's going on. It's a lot of walking for disabled people, it's disgusting."

Weary staff facing the wrath of angry passengers predicted things would only get worse during the Olympics.

A supervisor from contractor STM security helping to guide passengers said: "I tell you, London Bridge [station] will collapse [during the Games]. They don't have the capacity. I feel bad for all the people." The supervisor, who declined to give his name, said the 25 staff from STM had been given a 15-minute preparatory briefing on Tuesday morning. A Transport for London worker, who also wished to remain anonymous, said: "It's going to be like this every bloody day during the Olympics … The tourists are okay; they're patient but the commuters aren't."

As the day dragged on, police community support officers and British transport police officers also appeared to help manage the flow of people and signs were hastily erected showing people which direction to take, adding to the perception of inadequate planning.

Despite the complaints, a spokesman for Network Rail said the rehearsal had gone well and that due warning had been given. He added that there would have been little point staging the exercise if people had decided to change their travel plans because of the drill.

"He said Tuesday's test events would "give regular commuters the chance to get used to the way some of our busiest stations will work during the Games and allows us to make sure the plans we have in place are right".

The spokesman said that things had gone "smoothly" at all five stations, but suggested people should allow extra time for their journeys.

"I've got a team of people who've been at the station since 6am providing real-time information, plus I came through there at just after 7.30am, and they are saying that everything has gone as planned. I appreciate some people may have not enjoyed having to take a slightly longer route through the station but that is all we're asking people to do."

He also denied Network Rail had under-publicised the event in order to impress on people how overcrowded London Bridge would be during the Games.

Commuters are being advised to avoid the central London station altogether during the event.

Further disruption was caused on Tuesday morning after King's Cross St Pancras and Euston underground stations were closed during rush hour to prevent overcrowding after a Northern Line train broke down.